The beginning till the end
by sgathresholdxfiles
Summary: From Trees made of Glass to the unaired episode Headtrip and beyond. Long lasting relationships are built on trust and understanding. Will Molly and Cavennaugh be able to make it to the end...together?
1. Chapter 1

Disclaimer: I do not own 'Threshold' or any of the characters or related concepts

AN: Appreciate any feedback given and hope to continue this story on for many more chapters

Her life wasn't all that interesting. She worked full time for the government, had her dog, Monster, and lived in her home in Washington by herself. She hadn't dated anyone in several years and had a handful of friends who had slowly drifted apart over the years, all starting families and moving to different states. She considered herself a workaholic, using this as an excuse to not think about all the other stuff. The stuff her family always brought up whenever she visited them. She had an older brother and a younger sister, both of whom were married and had a handful of children themselves. They were a close family; however, their father wasn't around anymore. He'd disappeared without a trace when Molly and her siblings were all in their teens.

Everything changed that fateful night when she was approached by Sean Cavennaugh, a tall, handsome federal agent, regarding one of her most extensive contingency plans, one she thought would not be implemented any time soon, let alone in her lifetime. She heard the helicopter from a while away but thought nothing of it as Monster sniffed around the grassy oval.

"Okay, Monster, pick a spot" She said, waiting for the dog to do its business.

The sound grew louder and louder until she saw it lowering down close to her. Cavennaugh jumped out and made his way over to her and reached out to shake her hand.

"Molly Anne Caffrey? Name's Cavennaugh. Federal agent. One of your plans has just been activated. You're needed in Washington" He informed her.

"Which plan?" She asked.

"Threshold. You've just become the most important person on the planet." She stared at him in shock while Monster hid behind her, frightened by the noise of the helicopter.

"Will I have time to grab a few things? I live right over there." She pointed to her house.

"No time. We have to go now. Bring the dog with you." He reached out and softly touched her shoulder to guide her. She complied.

Threshold was a big deal. A contingency plan to resolve an Alien invasion and save all of humanity. Who would've thought that she would be the one to come up with such a plan? Well, her past certainly had some involvement in her career choice. She picked up Monster and they climbed into the helicopter.

Before she knew it, they were in the air and on their way to the Threshold building. Cavennaugh watched her closely. He was deep in thought. Many things were racing through his mind. He now had to protect this woman at all costs. He'd taken the job after reading through her protocols. He had always felt like he was meant for a larger purpose in life. By becoming the head of security at Threshold, he felt that purpose and importance. He would protect Molly Caffrey at all costs.

She caught him staring.

"What?" She asked. She knew nothing about this man but something about him already intrigued her. He didn't know what to say, so many things running through his mind.

"Nothing. Shouldn't be too much longer until we land." He looked out the window.

"Okay." She smiled, stroking Monster by her side to keep him calm.

They got to the building not too long afterward. J.T Baylock met them in the underground carpark and guided them upstairs to the meeting room where she advised a roomful of people, including her friend Andrea, who was the national security advisor.

She had skimmed over Threshold at times so she was still familiar enough with the plan that she didn't need to go over any details before the meeting began. She got right into it, explaining the situation regarding the mysterious object over the naval ship, the initial and first stages of the plan to assess the situation at hand and quarantine the area. Cavennaugh was impressed at how confident and knowledgeable she was and the fact that she just jumped straight into it.

After the meeting, Cavennaugh and Molly made their way to a smaller meeting room a few floors down to meet the red team.

Cavennaugh ran through each team member whilst they were walking.

First up, they had Nigel Fenway, microbiologist with a background in pathology. Next was Lucas Pegg, Astronautical Engineer, and last but not least, Arthur Ramsay, expert in linguistics and applied mathematics.

"If our ET needs to phone home, he'll translate the call," Molly mentioned. She was satisfied with her choices of initial phase red team members.

"Yeah, well he's also got a gambling, booze and a stripper problem."

"We all have our vices." She said. 

"Really? What are yours, Dr. Caffrey?" He tested her.

"I only reveal those on a need to know basis, Mr. Cavennaugh." She smirked.

They came to the outside of the room and stopped.

"Not exactly Charlie's angels, are they?" Cavennaugh commented, seeing the three men sitting behind the glass doors, accompanied by J.T Baylock.

The next few hours were intense. Molly explained the plan in detail to the red team, outlining their job titles, explaining the safety of their families and themselves as well as the seriousness of the situation in which they were now involved. The world depended on them.

Ramsay panicked but soon came to after Cavennaugh cornered him for a 'chat'. It wasn't long before they were again in the air on the way to the big horn ship taking their first look at what was left after the mysterious object in the sky.

Again, Molly caught Cavennaugh looking at her. This time he spoke first. "That your father's watch?"

She looked up at him. "What makes you ask that?"

"Tag Heuer Monaco. Steve McQueen wore one. If you were a guy back in the 70's, that was a must have item" He replied. She was impressed. She had worn that watch almost every day since the disappearance of her father.

"My dad thought so, too." She looked away. He could see a flash of pain reflecting in her eyes.

"He still around?" He asked.

"I don't know." He didn't want to push it. After all, they'd only know each other less than 12 hours.

The helicopter landed on the ship. Canvennaugh and his men checked the ship before allowing the others to leave the aircraft. Once containing Gunneson, the only crewman who appeared to have survived so far, they made their way onto the ship and down to the room where he was being held.

Gunneson was alive and in shock. He began explaining the events as they occurred. Lucas and Ramsay both shared worried looks. The events he was describing about the object in the sky sounded bizarre. While Fenway checked him over, Cavennaugh followed Lucas and Molly to the break room where the video tape was located. They watched as the tape started off with the crewmen joking around, having a good time, but then quickly changed to them being outside looking up to the sky where the object emitted a loud piercing noise. Their ears began to painfully ring. Molly could feel the intense pressure building up in her head.

"What's it doing? What's that sound?" Cavennaugh asked, concern showing all over his face.

"Agh!" Molly winced, noticing blood coming from Lucas's nose as he keeled over in pain.

Cavennaugh quickly grabbed his gun and shot at the video player. Their hearts were beating fast and their breathing was laboured.

"ARE YOU GUYS ALRIGHT?" Cavennaugh asked.

"Yeah…" Molly wiped the blood from her nose.

"Congratulations, gentlemen. We've just accomplished the first task of Threshold. Confirmation of extraterrestrial intelligence" She couldn't believe what she had seen. The sounds and shapes that object was forming in the sky. It was out of this world.

She noticed Lucas's panicked look. "Are you okay?"

He shook his head, wiping his nose.

"Come on, let's get cleaned up and get back to the others." She helped Lucas off the ground, keeping her hand on his back to comfort him. The poor guy looked absolutely shaken from the whole thing. Cavennaugh guided them back through the ship to safe zones.

Everyone continued on with their tasks. Lucas was sifting through data, Ramsay was busy working on the computer systems. Fenway was busy collecting samples and keeping an eye on Gunneson. Molly decided to step outside for some fresh air. She still had a slight headache from the videotape but it wasn't anything she couldn't handle. She was leaning on the rail on one of the decks when she heard footsteps.

"Any luck?" Cavennaugh approached. She had a feeling it was him. He seemed to be keeping a very close eye on her the whole time, not that she minded. It was somewhat comforting knowing he was always nearby, especially in their new circumstances.

"I've asked our naval escorts to do another sonar sweep but…so far, nothing." She sighed.

"So that thing on tape wasn't tracked leaving by air, not underwater…then where the hell did it go?"

"You nervous?"

"You really thrive on this crisis stuff, don't you?" He found it intriguing to see such a young woman so passionate about this kind of job.

She chuckled. "Is it that obvious?"

"Worst case scenarios…what kind of a person…picks that for a job description?" Surely there was more to it than just 'an obsession with her job', he thought to himself.

She looked up at him. "The kind of person who's lived through one." She turned and walked away. She barely knew this man and wasn't yet close to ready to share her past with anyone.

Cavennaugh watched her walk away. He wasn't really expecting her to share her past with him. He had skimmed over her file, as he suspected they all did about one another, but there wasn't much detail in there, just that her father disappeared without a trace when she was in her teens. There was mention of difficult circumstances for Molly, her siblings and their mother for several years after that.

Something about Molly really drew him in from the start. He wanted to find out about her past, to learn more about this woman, but he would be sure to be patient and supportive to her, whatever she decided to share with him in time.

The team began gathering their things. They didn't have much time left to gather what they could salvage before they blew up the ship. Molly wasn't happy about it but knew they couldn't have anyone else finding out about this. Whilst making their way back to the top deck, they had a run in with Gunneson. Cavennaugh fought but wasn't strong enough. He was knocked to the ground, leaving Molly helpless.

"Gunneson! Stay back!" She yelled, firing her weapon at him. Bullet after bullet. He was barely budging. Fear filled her insides. Then suddenly he turned and ran toward the side of the boat, jumping into the freezing cold water and disappearing. She looked over the edge for him but saw nothing. She quickly turned back around to where Cavennaugh was. She gently touched his shoulder.

"Are you okay?"

"Yes" He wiped the blood from his lip.

The ship was blown to pieces once they were in the air and far enough away.

The next few hours were debriefing and going over what they had discovered on the ship. Once done, Molly, Lucas and Cavennaugh were each checked over by Dr. Fenway.

Cavennaugh sat on the edge of the bed as he pulled on his shirt.

"Why don't you come back tomorrow afternoon and we'll run another round of tests' Fenway said, as Cavennaugh pulled the electrodes off his skin 'So what is that...a battlefield scar?"

Cavennaugh looked up at him, "Somethin like that"

"Whoever stitched you up should be making shoes for a living. Hey let me ask you something. I understand what I'm doing here, other's. What exactly is your job title...I mean who...who cuts your cheques? Fenway asked.

"I'm freelance. I do contract work" Cavennaugh replied cooly. He continued buttoning up his shirt, then began gathering his things. He could tell Fenway was trying to push his buttons however he had excellent self control and wouldn't give in to it.

"Oh….so you're a ghost. You're the guy they call in when they can't acknowledge they've sent someone in"

At that moment Molly walked up to the room, over hearing the last comment. Fenway and her didn't see eye to eye either however she would of course make an effort to be civil with him as he was a very important part of the team. She looked over at Cavennaugh to gauge his response but saw he maintained a straight face. He didn't look bothered by Fenway's comment at all. She smiled.

She decided to interrupt, curious to find out what Fenway had discovered.

"Should we be worried?" Both men turned around and saw her standing there. Blood rushed to Fenway's cheeks as he inwardly admitted to himself he had taken that a bit far.

"No I uh...haven't found any cellular damage or mutations"

"So we're clean?" Cavennaugh asked.

"Sort of,' Fenway moved over to the computer screens as they followed behind him, 'I picked up some sort of unusual activity in the mid to lower frontal lobes, both of you, Lucas too."

"Are you saying we're sick?" Cavennaugh said.

"No, no, no. We're talking brain wave activity. See these,' pointing to his screen 'these are theta waves. You're all generating far more than the average cognitive model"

"You're saying the video tape changed the way we think?" Molly asked.

"Maybe" Fenway said.

Molly looked over at Cavenaugh. He was staring at the screen.

"Anyway...uh...I can't see any reason to keep you here now. My advice, get some rest. Even ghosts need sleep right?" Cavennaugh didn't react once again.

Cavennaugh grabbed his jacket and walked out of the room. Molly followed right behind. He slowed down hearing her following behind him.

"Don't listen to Fenway...he's just…finding it hard to adjust" He slowed and smiled, turning to look at her.

"Don't worry…I've met plenty of guy's like him…old, lonely and angry at the world' She chuckled 'Anyway, I'm going to head home now. I'll see you in the morning" He squeezed her shoulder.

She stayed another hour, going through some notes on her computer before making her way home. She could barely keep her eyes open. As soon as she hit her bed, she was fast asleep.

The room suddenly felt dark, she knew this was a nightmare but she was trapped and couldn't escape. She suddenly saw glass everywhere, glass trees, a glass forest. A black, alien looking creature lurked in the darkness. Her heart raced as she looked around for an escape. There was no escape.

*Ring Ring*

The phone woke her from her sleep. She was covered completely in sweat and her heart was still racing. Her eyes even slightly filled with tears from the realness of the nightmare.

It was Cavennaugh. He'd had the same nightmare, he sounded just as shaken up as she was. As soon as he was off the phone she made her way to the kitchen. This was when the real nightmare began.


	2. Chapter 2

FLASHBACK:

Her father, Robert Caffrey, was a secretive man. He told his family that he worked as a security advisor at one of the largest banks in town, alongside his good friend and partner Jeff. His shifts were constantly changing. Sometimes he was required to go interstate, occasionally for weeks at time. They accepted it as it brought the money, although Molly could tell it upset her mother to have him gone for long periods at a time. When she was 12 years old, she heard her parents arguing one night.

"Why can't you tell me where you're REALLY going?" Her mother shouted in an accusing manner.

"What do you mean? Do you think I'm having an affair?" Her father retaliated.

"I don't know what to think. You're barely here these days and when you are here, you're distant. You've got bruises all over you, for God's sake! Don't tell me you ran into something or fell. I want the truth… or…" Molly could see the tears falling down her mother's face as she stayed hidden, peering slightly through the crack in the door.

"Or what…?" Her father lowered his voice.

Her mother shook her head and turned away.

"I never wanted this for any of you. There are things that I cannot tell you, but it is not what you think it is. I would never hurt any of you… I'm…" his voice cracked, "I'm doing this to protect you."

"I feel like I don't know you anymore. I know you have a dangerous job, but what's changed lately? Are you in some kind of trouble?" Concern etched her mother's face.

He didn't reply. She turned back around to face him when his phone buzzed. He hesitated, not wanting to end the conversation like this. The phone buzzed again so he pulled it from his pocket.

It was work. They needed him urgently, something was wrong and he had to go right away. He looked up at her, she whispered "Go..."

He walked over to her and pulled her into his arms. Molly wasn't sure what was going on but she could tell things weren't okay. She had tears forming in her eyes as she watched the scene unfold in front of her.

Her father kissed her mother, whispering "I love you. I love all of you very much and we will work this out together… as a family." He pulled back from her, squeezing her hands as he gathered his things and moved out the door. Molly ran back into her room. Her brother and sister were already asleep in their rooms. She sprung into her bed, pulling the covers over her head and pretending to be asleep. Her father did the rounds, saying goodnight to each of them, leaving Molly last but not least.

He walked into her room, smiling at his daughter. He knew she would do amazing things one day, she was very clever and smart for a 12 year old. He had a terrible feeling in his stomach that this may be the last time he saw her in a while.

He leant down and kissed her forehead, whispering. "There's no goal too big, darling daughter. Never let anything stop you from reaching your goals."

Molly kept her eyes shut tight, tears forming inside them. Her dad pulled away before taking his watch off and resting it on her bedside table. She heard the footsteps leaving her room and making their way downstairs before the front door opened and closed with a soft bang.

He got into his car and started the motor. His phone rang. Caller ID was Jeff. He answered the call.

"Rob… I hate to tell you this but… It's happening. They're here and they know where you are. You need to get to the safe zone right away!" Jeff told him.

"I had a bad feeling this would happen… I don't know how, but I just knew…." He paused and then finished with 'Please look after my family… promise me?"

"I will. I have men watching the house now and we'll organise to move them in the next few days."

The aliens were here. There may have been only a handful, but they were powerful and they wanted to extinguish Robert, as he was a major threat.

While on an assignment, he had come across a space craft. It wasn't all that large so they were able to transport it to a holding facility within a day, before transferring to an underground bunker in Alaska that was built specifically in the event of an Alien abduction.

It wasn't the craft itself that interested them all, it was what they found inside. Plans to take over Earth. There were diagrams, detailed in several hundred pages. They decided to get a head start on the ship and check it over while it was in the holding facility in Minnesota.

Robert made a huge mistake, though. He couldn't resist pressing just one button. The scientists were too busy rummaging around the ship to notice. Suddenly a screen turned on in front of him. What he saw almost scared the daylight out of him. Aliens. They were black, roach looking creatures.

The scientists looked up in shock and horror. Robert was frozen, staring at the screen as the creatures peered back at him. Suddenly a flash. He winced and pulled away, rubbing his eyes.

"You have our ship. We will find and destroy you, human." The creature said in a snarly voice.

They were pissed off. One, because they had their ship. Two, because now the humans knew their plans to take over Earth, so they could prepare for it.

One of the scientists jumped up and pressed another button. The screen turned off.

"What have you done?" The scientist turned to Robert.

"I… I have to go." He ran out of there as fast as possible. The scientists removed all wire connections to the screen and made sure to cut out any power to the ship to avoid any more transmissions.

He had several meetings with his superiors over the next few days. They had advised that he take some time off but he insisted he keep on working. He needed to find out as much as he could about these Aliens, about their plans for Earth. The aliens were already here. They had taken over a small selection of humans. Robert started to notice strange things happening to him over the next few months. People were watching him, following him in his car.

He thought he was just being paranoid until one of them attacked him one night while he was leaving work. Luckily, Jeff had forgotten to give him something during the day and shot the attacker. When the man didn't fall to the ground, he shot again and again until he eventually fell to the ground. They dragged the man inside and heavily sedated him. The agency ordered that the man to be transferred to Alaska to be held in a facility where he would be constantly under sedation so tests could be done.

Robert was startled by the event but had no idea this would affect his entire life so much. It was hard enough being a secret agent and not being able to tell your family anything.

This was the last time any of them saw him. He never returned home the next day. The next night, her mother received a phone call from Jeff. Jeff had tried to check in with the agents guarding their house, but after no response, he knew something bad was about to happen.

"Anne, I just received a call from... you need to get the kids and hide!" He spoke fiercely.

"Jeff! What are you talking about? What the hell is going on?" She jumped out of bed straight away, knowing something was very wrong. She moved into each of the kids' rooms and shook them awake.

They didn't have a clue what was going on and were disorientated from being asleep, but they complied and followed her. Molly's room was at the end of the hallway. They all stood in there waiting for their mother to speak. Jeff was still on the other end of the phone.

"Have you got all the kids with you?"

"Yes. But-"

"I'll explain everything later. I promise… but right now you all need to hide." Jeff told her.

Before they could say any more, there was a loud smashing sound from downstairs. Molly's younger sister Amy screamed, while her mother quickly covered her mouth to dull the sound.

"Shhh, baby. You need to stay quiet, okay?" Molly's brother Ben thought quickly as they heard men shouting from downstairs. "CHECK UPSTAIRS! GO!" They heard the sound of men's heavy boots thud up the stairs.

"Quick, we need to hide." Ben said to them all. Her mother gathered them and they ran to the closet. They closed the door as quietly as possible and moved toward the back of the closet. There was a secret door inside there. Anne quickly punched in the code and the door unlocked. She opened the door and ushered them inside. It was small, very small, actually, but it would fit the three kids. That was her main priority.

It all happened so fast. There was a bright light, the cupboard door opened and two men stood in front of them all with guns pointed at them. Anne slammed the door closed as the kids screamed. The gunshots rang through the air as their mother screamed.

The men smashed up the house, searching eagerly for the item that her father had left behind. However, they did not have enough time. Before they knew it, the FBI were all over the house like a rash. They shot and captured all of the intruders. They found Anne Caffrey upstairs with two gunshot wounds, bleeding heavily from her shoulder and back.

Agent Jackson ran over to her and checked her pulse, looking up at his partner Agent Moore.

"SHE'S ALIVE!…barely." He shouted, putting pressure on her back wound while the other agent grabbed a towel to help put pressure on the other wound.

The quiet sobs could be heard from inside the closet. More agents filled the room as paramedics followed, moving their mother onto the gurney as they hooked her up to oxygen immediately.

"Jackson. Do you hear that? It's coming from inside there." They saw the door slightly ajar and slowly opened it. What they saw inside broke their hearts. The poor kids were traumatised. The agents moved the kids out of the space as quickly as possible to keep them from seeing the bloody scene, softly speaking comforting words to them.

This was a night they would remember for the rest of their lives. They each had to undergo counselling for the next 6 months and never returned to their house. They had body guards looking out for them wherever they went. Their mother survived the wounds however was paralysed from the waist down after the gunshot wound to her spine. As she was too unwell to leave the hospital, and all the kids were under the age of 18, they were put into a foster care home temporarily until one of Anne's long-term friends stepped up and applied for a temporary guardianship of the three kids.

The next few years were hard, the kids all received counselling twice a week. They never found her father. Never found out why he disappeared. Jeff hadn't told Anne what he knew as he was sworn to secrecy however he was there supporting them through it all as best he could.

END FLASHBACK:


	3. Chapter 3

The dreams were intense. Cavennaugh had called her the night after they had returned from the Bighorn ship. What he had described to her on the phone was identical to the dream, or more so nightmare, that she had, too. She had gotten up to get something to drink from her fridge when Gunneson appeared out of nowhere. He attacked her but she fought back and eventually knocked him over the head with a shovel. When Cavennaugh's men came and tried to recover his body, he was gone. Vanished into thin air. This scared her more than anything. _How was she supposed to stay in her house after the attack_ , she thought to herself?

She didn't have time to worry, though, she had a job to do and the entire population relied on her.

Cavennaugh spotted her in the break room. She looked up at him and smiled as she stood up from her seat.

"Here, keep it." He pulled one of his guns out of the holster and handed it to her.

"Don't you need it?" She asked.

"I carry two." Of course he did, she was surprised he didn't have more than that on him.

She scoffed, "You gave me the girl gun."

"A revolver is more reliable,' he grabbed the gun back from her, demonstrating its ease of use, 'It won't jam like an automatic. When we have time I'll take you to the range." 

"I shot Gunneson 4 times and it didn't even slow him down." 

"Yeah, well after what happened on that ship, I've had all the ordinances switched to explosives… it should cause a lot of more damage. Now I want you to aim for the ten spot, the heart. Okay? If your aim was better, you could have put him down for good." He looked at her intensely.

"My aim was good enough to save your life." She smirked.

"It's not mine I'm worried about" He walked off. She sighed. She appreciated the fact that he was so worried about everyone else, but who worried about him?

She spotted him from down the hallway, walking towards her.

"Hey. Are you free tonight after work?" He asked her. He didn't waste any time.

"Yeah, what's up?"

"Well… I was going to see if you'd be up for those shooting lessons I mentioned earlier. I figure the sooner you learn to shoot, the better."

"Sure. That would be great. I'll meet you here at say, 7?"

"Perfect. I'll see you then." He left, leaving her smiling. She would feel a whole lot safer if she knew how to shoot a gun properly.

Molly came out of the elevator and made her way to the range on the 5th floor. She opened the door and made her way inside. Cavennaugh was already there, setting up a few different handguns and lining them up for her. He turned around and saw her.

"You ready?"

"As ready as I'll ever be." She was looking forward to this.

He stood up right behind her. He seemed to have no issue invading her personal space at all.

"Okay. First thing, you want to make sure you're as relaxed as possible. As soon as you tense up, the recoil is going to be more intense." He placed his hands on her shoulders and she relaxed. He moved one hand to her waist, slightly turning her body so that her right foot was in front. She could smell his warm musky scent when he was this close to her. It was driving her crazy. _Makes it hard to relax when you're pressed right up against me,_ she thought to herself.

She nodded, acknowledging what he said.

"Can I shoot something now?" She asked, turning her head slightly toward him. He removed his hands from her, giving her some space to adjust her stance and get comfortable.

"Okay. When you're ready, pull the trigger." He instructed. They both pulled their earmuffs on.

She pulled on the trigger and the bullet shot through the air, hitting the target. She smiled, feeling proud of herself. Cavennaugh nodded, impressed with her aim. She did have a pretty good aim for someone that had barely any firearm training.

"Not bad…not bad at all. Now try looking down the top of the barrel." He pointed to where she was to be looking down on the gun and she squinted, lining up her next shot.

She nodded as he stayed closer to her this time. He rested one his left hand on her hip, keeping her steady. She shivered slightly under his touch. Luckily, he didn't seem to notice. She thought him distracting her would put her off but this time she hit closer to the bull's eye.

He stayed close, helping her to reload the guns. He showed her a few other guns while they were there so she would feel comfortable if she ever needed to use something different for whatever reason.

The next couple of hours seemed to fly.

"I think you're almost better than some of my guys." Cavennaugh said.

"What can I say? I'm a natural." She said coolly, stepping back.

He laughed and then grabbed one of the gun's. Molly folded her arms over her chest as she watched. He shot the gun 5 times, hitting the bullseye 4 out of 5 times. He was good. Very good. He pulled his ear protection off his head and turned to her.

"Not bad…" She commented.

He grabbed the empty guns, handing her a few to carry back to the safe.

"You think I'm ready for the field yet?" She joked.

"As long as I'm there to back you up, sure." He said, leading her out with his hand on her lower back as always.


End file.
